IsoformSwitchAnalyzeR 0.99.11
Kristoffer Vitting-Seerup
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IsoformSwitchAnalyzeR | | Last Changed Rev: 130219 / Revision: 131943 | | Last Changed Date: 2017-06-09 05:31:13 -0400 (Fri, 09 Jun 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IsoformSwitchAnalyzeR_0.99.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘0.99.11’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IsoformSwitchAnalyzeR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 4.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createSwitchAnalyzeRlist: no visible global function definition for
'Rle'
expressionAnalysisPlot: no visible binding for global variable
'Condition'
expressionAnalysisPlot: no visible binding for global variable
'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
'CI_down'
expressionAnalysisPlot: no visible binding for global variable
'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceSummary: no visible binding for global variable
'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
'geneFraction'
extractConsequenceSummary: no visible binding for global variable
'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
'isoFraction'
extractConsequenceSummary: no visible binding for global variable
'nrIsoWithConsequences'
extractGenomeWideAnalysis: no visible binding for global variable
'isoform_feature'
extractGenomeWideAnalysis: no visible binding for global variable
'value'
extractGenomeWideAnalysis: no visible binding for global variable
'variable'
extractGenomeWideAnalysis: no visible binding for global variable
'ymax'
extractGenomeWideAnalysis: no visible binding for global variable
'significance'
extractGenomeWideAnalysis: no visible binding for global variable
'idNr'
switchPlotTranscript: no visible global function definition for
'queryHits'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
Undefined global functions or variables:
CI_down CI_hi CI_low CI_up Condition Domain IF Rle geneFraction
gene_expression idNr isoFraction isoform_feature
nrGenesWithConsequences nrIsoWithConsequences queryHits sigEval
sigLevel sigLevelPos significance switchConsequence value variable x
xmax xmin y yend ymax ymin
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoformSwitchAnalysisCombined 24.670 0.195 25.589
IsoformSwitchTestDRIMSeq 20.757 0.253 21.533
isoformSwitchAnalysisPart1 16.273 0.074 16.820
analyzeIntronRetention 9.209 0.025 9.540
importCufflinksData 8.720 0.134 9.139
importRdata 6.992 0.128 7.366
switchAnalyzeRlist 6.657 0.105 6.985
extractGenomeWideAnalysis 6.432 0.121 6.736
isoformSwitchAnalysisPart2 5.213 0.083 5.443
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘pheatmap’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
* DONE (IsoformSwitchAnalyzeR)